Contacts of the strand formed by residues 26 - 31 (chain F) in PDB entry 5A15


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with VAL 26 (chain F).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     24F  PRO*     4.0    14.7    -      -       -      +
     25F  GLU*     1.3    86.5    -      -       +      +
     27F  VAL*     1.3    63.9    +      -       -      +
     28F  GLU      4.1     0.7    +      -       -      -
     37F  PHE*     4.3    19.1    -      -       +      -
     38F  THR*     3.4    24.0    -      -       -      +
     39F  ARG*     4.5    15.0    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 27 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     23F  PHE*     5.3     3.1    -      -       +      -
     24F  PRO*     4.2    17.5    -      -       +      +
     26F  VAL*     1.3    78.5    -      -       -      +
     28F  GLU*     1.3    67.1    +      -       -      +
     29F  LEU*     3.8     4.9    +      -       +      +
     36F  TYR      3.8     0.5    -      -       -      +
     37F  PHE*     3.6     4.4    -      -       -      -
     38F  THR*     2.8    36.1    +      -       +      +
     40F  HIS*     4.1    33.9    -      -       +      -
     43F  LEU*     4.4    13.0    -      -       +      -
     55F  PHE*     3.9    15.0    -      -       +      -
     73F  PHE*     3.8    32.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with GLU 28 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     26F  VAL      4.1     1.6    +      -       -      -
     27F  VAL*     1.3    79.6    -      -       -      +
     29F  LEU*     1.3    60.7    +      -       -      +
     35F  VAL*     3.6    13.2    -      -       +      +
     36F  TYR      3.8     2.9    -      -       -      -
     37F  PHE*     3.1    42.2    -      -       +      -
     72F  ARG*     3.2    45.2    +      -       +      +
     73F  PHE*     3.7    19.6    +      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 29 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     27F  VAL*     3.8     7.1    +      -       +      +
     28F  GLU*     1.3    72.4    -      -       -      +
     30F  ASN*     1.3    60.6    +      -       -      +
     31F  VAL*     4.2     9.6    -      -       +      -
     35F  VAL*     3.2    10.1    -      -       -      +
     36F  TYR*     2.9    42.7    +      -       +      +
     38F  THR*     5.8     6.3    -      -       +      -
     43F  LEU*     6.2     4.9    -      -       +      -
     55F  PHE*     5.9     5.2    -      -       +      -
     72F  ARG*     4.9     1.8    -      -       -      -
     73F  PHE*     3.7     9.9    -      -       +      +
     75F  ILE*     5.6     5.6    -      -       +      -
     82F  PHE*     5.4     5.8    -      -       +      -
----------------------------------------------------------
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Residues in contact with ASN 30 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29F  LEU*     1.3    74.1    -      -       -      +
     31F  VAL*     1.3    56.6    +      -       -      +
     33F  GLY*     3.1    30.0    +      -       -      -
     34F  GLN      3.4     3.8    +      -       -      +
     35F  VAL*     4.4     7.0    +      -       +      +
     68F  ASP*     3.6    22.4    +      -       -      +
     72F  ARG*     4.5     9.8    -      -       +      +
     73F  PHE      2.7    17.0    +      -       -      +
     74F  PHE*     3.3    26.8    -      -       +      -
     75F  ILE*     2.7    32.6    +      -       -      +
     37G  PHE*     3.5    24.4    -      -       -      -
----------------------------------------------------------
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Residues in contact with VAL 31 (chain F). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
     29F  LEU*     5.0     4.3    -      -       +      -
     30F  ASN*     1.3    75.9    +      -       -      +
     32F  GLY*     1.3    58.0    +      -       -      +
     33F  GLY      3.0     2.9    -      -       -      -
     34F  GLN*     2.9    31.0    +      -       -      +
     36F  TYR*     4.5     3.1    -      -       +      -
     75F  ILE*     3.3    24.9    -      -       +      +
     77F  ARG*     3.4    28.0    -      -       +      +
     78F  ASP      3.7    14.1    -      -       -      +
     79F  GLY*     3.0    16.7    -      -       -      -
     82F  PHE*     3.7    46.2    -      -       +      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il